Diffusion may keep big knots out of DNA

Snapshots of a new computer simulation, left, show how two knots along a strand of DNA can slide past one another without becoming entangled. A simplified represenation, right, shows how the red knot loosens and the green knot spreads along one of the loops to pass through.

DNA can get knotted naturally, and scientists have previously tied artificial loops into molecules of genetic material. Now, a team has created a computer simulation that shows how two knots on a strand of DNA can pass through each other without adding any additional snarls. One knot loosens while the other spreads along the curves of the first one and moves through it.

The way the knots pass through each other could play a role in sequencing DNA on nanopores once the strand sizes get bigger than 100,000 base pairs, the scientists report May 19 in the Proceedings of the National Academy of Sciences.